DNAunion: Concerning whether or not the abiotic production of amino acids is easy or difficult, its closer to the easy side.
STRECKER SYNTHESIS
The main method of amino acid formation mentioned in OOL material is the Strecker synthesis named after the scientist who first used it to create the amino acid alanine. As far as reactants are concerned, it requires the following:
1) hydrogen cyanide (HCN)
2) ammonia (NH3)
3) an aldehyde (R-COH)
HCN is considered to have been extremely abundant in prebiotic times (actually, theres something that challenges that assumption, but Ill ignore it for this discussion), and the other two are also considered to have been plentiful (though possibly to a lesser extent).
In the original synthesis of an amino acid by Strecker, the aldehyde used was actetaldehyde, which produced the amino acid alanine. But for the simplest case, well use formaldehyde (R = H, giving H-COH).
HCN + NH3 + H-COH <-> H2C(NH2)CN + H2O
H2C(NH2)CN + H2O -> H2C(NH2)CO(NH2)
H2C(NH2)CO(NH2) + H2O -> (NH2)CH2(COOH) + NH3
Where (NH2)CH2(COOH) is the simplest amino acid, glycine.
GETTING AMINO ACIDS NOT THE PROBLEM
The Strecker synthesis is believed to be the source of most of the amino acids that have been found in meteorites. It is also the pathway by which amino acids were formed in the Stanley Miller electric-discharge-in-a-highly-reduced-atmosphere experiment. In addition, IIRC, free amino acids (i.e., external to any organisms) have been found at deep-sea hydrothermal vents (though I dont recall by what method they are supposed to have been produced).
So the real problem for prebiotic chemistry in relation to proteins is not getting amino acids to form, its a combination of (1) getting only the correct amino acids and (2) getting those correct amino acids to polymerize into proteins.
(1) Getting the correct amino acids
HOMOCHIRALITY
19 of the 20 (primary) biological amino acids are chiral, meaning that they have both a left-handed and a right-handed version. For a given chiral amino acid, the two optical isomers are mirror images of each other, but are not superimposible one upon the other, and are therefore called enantiomers. To get an idea, think about your left and right hands they are mirror images of each other but there is no way that you can orient them such that they are superimposible (the closest you can get is palm-to-palm, but then the knuckles of one hand point in one direction say left and the knuckles of the other hand point in the opposite direction say right). Note that both enantiomers of a given amino acid have identical chemical and physical properties.
In biology, the rule is that only left-handed amino acids are used during protein synthesis. In biological terms, a protein is a linear, unbranched chain of left-handed amino acid residues bonded together by peptide bonds, with the chain folding up into a stable three-dimensional conformation that performs a particular biological function. This restriction to using only one of the two (chemically and physically equivalent) chiral forms of a molecule is called homochirality.
OOL researchers have stated that for life to arise, the polymers that kickstarted it (be they nucleic acids or proteins) needed to be composed of homochiral monomers (i.e., for proteins, to have all the same enantiomeric forms of amino acids, such as all left-handed).
But natural processes produce racemic mixtures of amino acids. A racemic mixture (or racemate) contains equal quantities of both enantiomers. Thus, in general, for every 1,000 left-handed lysine molecules nature would produce in a given microscopic environment it would also produce 1,000 right-handed lysines.
But if nature produces both enantiomers in equal amounts, how did the first proteins manage to have all left-handed amino acids?
Here comes the part most people object to probability calculations. I admit theyre not perfect, but hey, we gotta have some kind of idea of whats going on.
Suppose a protein capable of a useful function for our purposes, self-replication - needed to be at least 50 amino acids in length. Each of those 50 positions could be occupied by either an L-amino acid or a D-amino acid (L is levo, or left-handed; D- is dextro, or right-handed). Assuming equal likelihood of incorporation for both the L- and D- forms (since they have identical chemical and physical properties), the probability of obtaining a chain of 50 all-left-handed amino acids is 2^50, or about 10^15. So in general, youd need 10^15 randomly generated amino acid sequences to have a 50% chance of getting at least one that was all left-handed.
Let me address a counterargument sometimes heard. The original argument is that having both enantiomers makes it less likely to hit upon a functional sequence because you first have to get all left-handed ones before you can even think about getting the correct sequence. But wouldnt having more types more shapes -- of building blocks to work with make it possible to have more ways to construct a functional three-dimensional shape for a polypeptide? Yes, it would. But theres a problem
although the number of possible functional arrangements increases, the number of non-functional arrangements increases to a much greater degree. Let me try using an analogy.
Lets start with the numbers 0 19, with each representing one of the twenty biological amino acids. You need a polypeptide just two units long and it will function if the sum of those two numbers equals 10. So functional sequences include 0+10, or 1+9, or 2+8,
, 9+1, 10+0. There are 11 possible functional sequences in all. But with two slots and 20 possibilities for each slot there are 20^2 = 400 possible sequences in total. So the probability of hitting upon a functional sequence in one random shot is 11/400, or about 0.0275.
Now lets throw in the other enantiomers that is, lets include the mirror opposites of the numbers used above. With the addition of the negative numbers -1 through -19, there are now many more ways to get a functional sequence: 19+(-9), 18+(-8),
, -8+18, and -9+19. So yes, we now have more than double the number of correct combinations, going from 11 to 29. But
we now have 39 possibilities for each slot, not 20. So there are now 39^2 = 1521 possible combinations in all. Our probability of success has dropped from 0.0275 down to 29/1521 = 0.00986. Weve lost ground.
SEQUENCE INFORMATION
But theres more. Theres no good reason to believe that that ONE 50-aa polypeptide formed would be capable of performing self-replication. What is needed is a
very specific sequence in order to perform this function, not just any old sequence. Though science still does not know exactly how small the probability of hitting up a self-replicating peptide is (since no actual self-replicating proteins are known), it is difficult to do accurate calculations. So we must accept that the range of inaccuracy increases yet again with the next calculations.
Let us assume that only 1 in 10^20 all-left-handed-aa polypeptides 50 units long are capable of self-replication (I am intentionally vastly overestimating the power of proteins here I dont expect to be quoted on this value).
Combining the two previous crude calculations we end up with needing 10^15 x 10^20 = 10^35 randomly generated polypeptides to have a 50% chance of hitting upon at least one that could self-replicate (and again, I am probably vastly overestimating the power of proteins here, to err on the side of caution).
OTHER AMINO ACIDS
So far we have looked at getting only the left-handed forms of the 20 biological amino acids, and producing a functional sequence. But theres more to the story. Why only consider the 20 biologically relevant amino acids? In a prebiotic context, all aas that were present should be considered. And guess what? There are hundreds of different types of amino acids (this does not count left- and right-handed forms at two, but as one). And the Miller experiment and examinations of meteorites both show that more of the
non-biologically relevant amino acids are produced by natural processes.
FINAL ROUGH CALCULATION
Lets pull all of this prebiotic amino acid stuff together to formulate one overall probability. Here are the assumptions.
1) From a prebiotic racemic mixture, only left-handed amino acids get incorporated into the protein
2) From a prebiotic mixture containing roughly equal amounts of 40 different types of amino acids, only the 20 biologically relevant ones get incorporated into the protein
3) A self-replicating protein (capable of evolving) must be at least 50 amino acids in length
4) 1 in 10^20 proteins that meet the above criteria (only the left-handed enantiomers of the 20 biologically relevant amino acids are bonded together, 50 in all) can self-replicate.
Each slot has 80 possibilities (40 types of amino acids x 2 enantiomers each = 80). With 50 slots altogether, the probability of getting a self-replicating protein in a single random attempt is
P(replicator) = 1 in 80^50 = 1 in 1.427 x 10^95.
And yet theres more. We have to keep in mind that this assumes amino acids react only with other amino acids. As examinations of meteorites have shown, non-biological process create a witches brew consisting of all sorts of molecules. Some such as sugars would react with the amino acids and preclude them from making it into a protein. Other organic molecules would tend to terminate one end of the growing chain, thus halting elongation of the polypeptide.
All in all, getting a self-replicating protein from truly prebiotic conditions doesnt look very promising (and, getting a self-replicating RNA may be even worse at least the monomers of proteins are prebiotically plausible!).
(2) Getting those correct amino acids to polymerize into proteins
This topic was short changed in the above it was simply assumed that amino acids could be polymerized into proteins. But how? Here are some general concepts to keep in mind.
In aqueous solutions the thermodynamic tendency is for hydrolysis not dehydration synthesis - to occur. Yet it is the latter (also called condensation) that is involved in the joining together of two amino acids. The carboxyl group (-COOH*) of one aa reacts with the amino group (-NH2*) of another aa to form a bond, and in doing so, the equivalent of one molecule of water is removed (OH from one and H from the other, forming H2O). Drying conditions not aqueous solutions - favor dehydration synthesis.
So why not just throw heat energy at amino acids? Actually, that works
well, kind of. The high temperature removes excess water and adds energy that can drive bond formation. However, the resulting stuff isnt proteins, its proteinoid. The only point I will make here is that the resulting chains are highly branched, not linear. Why? Remember how I stated that amino acids bond by the carboxyl group of one aa reacting with the amino group of another? Well, some of the amino acids have these same functional groups on their side chains. Thus, instead of joining only end-to-end, amino acids can join side-to-end, messing up the linear series. In fact, one amino acid can join end-to-end with one amino acid, and side-to-end with another, thus forming branches. So instead of having a linear chain, you have get a branched and mangled chain.
THE END
*NOTE: Some biology books list these functional groups as COO- and NH3+ for amino acids, because at cellular pH, they become ionized.
PS: I came back to emphasize that my probability calculation is not meant to be definitive or accurate.
